Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells

Kenneth J Livak; Quin F Wills; Alex J Tipping; Krishnalekha Datta; Rowena Mittal; Andrew J Goldson; Darren W Sexton; Chris C Holmes

doi:10.1016/j.ymeth.2012.10.004

Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells

Kenneth J Livak, Quin F Wills, Alex J Tipping, Krishnalekha Datta, Rowena Mittal, Andrew J Goldson, Darren W Sexton, Chris C Holmes

Research output: Contribution to journal › Article › peer-review

122 Citations (Scopus)

Abstract

The stochastic nature of generating eukaryotic transcripts challenges conventional methods for obtaining and analyzing single-cell gene expression data. In order to address the inherent noise, detailed methods are described on how to collect data on multiple genes in a large number of single cells using microfluidic arrays. As part of a study exploring the effect of genotype on Wnt pathway activation, data were collected for 96 qPCR assays on 1440 lymphoblastoid cells. The description of methods includes preliminary data processing steps. The methods used in the collection and analysis of single-cell qPCR data are contrasted with those used in conventional qPCR.

Original language	English
Pages (from-to)	71-9
Number of pages	9
Journal	Methods
Volume	59
Issue number	1
DOIs	https://doi.org/10.1016/j.ymeth.2012.10.004
Publication status	Published - Jan 2013

Keywords

Cell Line
Data Interpretation, Statistical
Gene Expression Profiling
Humans
Limit of Detection
Lymphoid Progenitor Cells
Real-Time Polymerase Chain Reaction
Reverse Transcriptase Polymerase Chain Reaction
Single-Cell Analysis
Wnt Signaling Pathway

Access to Document

10.1016/j.ymeth.2012.10.004

Cite this

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title = "Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells",

abstract = "The stochastic nature of generating eukaryotic transcripts challenges conventional methods for obtaining and analyzing single-cell gene expression data. In order to address the inherent noise, detailed methods are described on how to collect data on multiple genes in a large number of single cells using microfluidic arrays. As part of a study exploring the effect of genotype on Wnt pathway activation, data were collected for 96 qPCR assays on 1440 lymphoblastoid cells. The description of methods includes preliminary data processing steps. The methods used in the collection and analysis of single-cell qPCR data are contrasted with those used in conventional qPCR.",

keywords = "Cell Line, Data Interpretation, Statistical, Gene Expression Profiling, Humans, Limit of Detection, Lymphoid Progenitor Cells, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, Single-Cell Analysis, Wnt Signaling Pathway",

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AU - Livak, Kenneth J

AU - Wills, Quin F

AU - Tipping, Alex J

AU - Datta, Krishnalekha

AU - Mittal, Rowena

AU - Goldson, Andrew J

AU - Sexton, Darren W

AU - Holmes, Chris C

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KW - Cell Line

KW - Data Interpretation, Statistical

KW - Gene Expression Profiling

KW - Humans

KW - Limit of Detection

KW - Lymphoid Progenitor Cells

KW - Real-Time Polymerase Chain Reaction

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